Effect of Terminal Phosphate Groups on Collisional Dissociation of RNA Oligonucleotide Anions.

The increasing need for mass spectrometric analysis of RNA molecules calls for a better understanding of their gas-phase fragmentation behaviors. In this study, we investigate the effect of terminal phosphate groups on the fragmentation spectra of RNA oligonucleotides (oligos) using high-resolution mass spectrometry (MS). Negative-ion mode collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD) were carried out on RNA oligos containing a terminal phosphate group on either end, both ends, or neither end. We find that terminal phosphate groups affect the fragmentation behavior of RNA oligos in a way that is dependent on the precursor charge state and the oligo length. Specifically, for precursor ions of RNA oligos of the same sequence, those with 5'- or 3'-phosphate, or both, have a higher charge state distribution and lose the phosphate group(s) in the form of a neutral (H3PO4 or HPO3) or an anion ([H2PO4]- or [PO3]-) upon CID or HCD. Such a neutral or charged loss is most conspicuous for precursor ions of an intermediate charge state, e.g., 3- for 4-nt oligos or 4- and 5- for 8-nt oligos. This decreases the intensity of sequencing ions (a-, a-B, b-, c-, d-, w-, x-, y-, z-ions) and hence is unfavorable for sequencing by CID or HCD. Removal of terminal phosphate groups by calf intestinal alkaline phosphatase improved MS analysis of RNA oligos. Additionally, the intensity of a fragment ion at m/z 158.925, which we identified as a dehydrated pyrophosphate anion ([HP2O6]-), is markedly increased by the presence of a terminal phosphate group. These findings expand the knowledge base necessary for software development for MS analysis of RNA.

[Establishment and transfer management of veno-arterial extracorporeal membrane oxygenation in patients with difficult downtime during cardiopulmonary bypass surgery].

OBJECTIVE: To investigate the establishment method, coordination points and safe transport management strategy of vena-arterial extracorporeal membrane oxygenation (VA-ECMO) in patients with downtime difficulties during cardiopulmonary bypass (CPB). METHODS: A observation study was conducted. The patients admitted to the department of critical care medicine of the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital) from January 2020 to October 2022 were enrolled. These patients could not be separated from CPB and received VA-ECMO-assisted CPB surgery. The clinical data of the patients were recorded, including the basic information of the patients, the data of VA-ECMO establishment and transport process, the clinical indicators before and after VA-ECMO installation, the operation data of VA-ECMO and clinical outcomes. The experience was summarized from the aspects of extracorporeal membrane oxygenation (ECMO) establishment, transport process, team cooperation, and adverse events during transport. The clinical indicators before and after ECMO operation were compared. According to whether ECMO was successfully weaned, the patients were divided into a successful weaning group and a failure weaning group, and the clinical data between the two groups were compared. RESULTS: Eighteen patients who underwent VA-ECMO-assisted CPB were enrolled, including 10 males and 8 females. The average age was (56.7±12.3) years old. Preoperative left ventricular ejection fraction (LVEF) was 0.46±0.10, and the main reasons for switching to VA-ECMO assistance included right ventricular systolic weakness in 6 cases, total cardiac systolic weakness in 5 cases, left ventricular systolic weakness in 4 cases, high pulmonary arterial pressure in 2 cases, and intractable ventricular fibrillation in 1 case. Among the 18 patients transferred from CPB to VA-ECMO, 10 cases were successfully weaned and 8 cases failed. In ICU, 8 cases survived, 5 cases died, and 5 cases gave up treatment and discharged. The average time for successful CPB to VA-ECMO establishment was (24.6±7.4) minutes, initial blood flow was (3.3±0.4) L/min, and transit time was (8.4±1.5) minutes. ECMO-assisted duration averaged (82.0±69.3) hours. Adverse events occurred in 9 patients during ECMO establishment and transfer. Post-ECMO onboarding for 4 hours, significant improvements were noted in blood lactic acid (Lac), pH value, mean arterial pressure (MAP), central venous oxygen saturation (ScvO2) as compared with pre-ECMO onboarding [Lac (mmol/L): 10.5±7.0 vs. 15.2±6.8, pH value: 7.38±0.92 vs. 7.26±0.87, MAP (mmHg, 1 mmHg ≈ 0.133 kPa): 74.9±13.7 vs. 58.4±17.0, ScvO2: 0.678±0.065 vs. 0.611±0.061, all P < 0.01], and vasoactive-inotropic score (VIS) was also decreased (39.8±29.8 vs. 68.9±64.4, P < 0.01). Compared with successful weaning group, the patients in the failed weaning group exhibited higher pre-machine Lac (mmol/L: 18.8±7.8 vs. 12.3±4.3, P < 0.05), longer CPB time [minutes: 238.0 (208.8, 351.2) vs. 200.0 (185.8, 217.0), P < 0.05], and shorter ECMO-assisted time [hours: 19.5 (11.0, 58.8) vs. 94.5 (65.8, 179.8), P < 0.01]. However, there was no statistically significant difference in pre-machine pH value, ScvO2, MAP, VIS score, and initial blood flow and establishment time of ECMO between the two groups. CONCLUSIONS: VA-ECMO is an effective circulatory aid for CPB surgery that cannot be weaned after CPB. The establishment and transfer of CPB "bridge" to ECMO aid depends on multi-disciplinary treatment (MDT) cooperation. The success rate of ECMO weaning is related to the Lac and CPB duration. If it is not possible to detach from the CPB successfully, VA-ECMO should be initiated as early as possible.

Effects of Different Carbon and Nitrogen Ratios on Yield, Nutritional Value, and Amino Acid Contents of Flammulina velutipes.

The carbon-to-nitrogen (C/N) ratio in the cultivation medium significantly influences the growth rate, vigor of mycelium, yield of fruiting bodies, and their nutritional composition. Recently, agricultural and forestry wastes have been increasingly used in cultivating Flammulina velutipes. However, systematic research on how these materials affect the nutritional and functional properties of the fruiting bodies is lacking. This study investigated the effects of different C/N ratios on F. velutipes cultivation. We evaluated the agronomic traits, nutritional composition, and flavor compounds of the fruiting bodies. Our findings reveal that an optimal C/N ratio of 27:1 in the composted substrates enhances the total yield of fruiting bodies, with 25.1% soybean straw as the primary raw material. This ratio also significantly increases the levels of crude protein, total amino acids, and essential amino acids in the fruiting bodies (p < 0.05). Fruiting bodies from the high-nitrogen (HN) treatment showed the highest content of umami amino acids and equivalent umami concentration value. Additionally, we employed an untargeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics approach to analyze the metabolite profiles of fruiting bodies cultivated in high-nitrogen (HN), medium-nitrogen (MN), and low-nitrogen (LN) substrates. We found that the carbon-nitrogen ratio can affect the flavor and quality of fruiting bodies by regulating amino acid biosynthesis and metabolism and other related pathways. Our results suggest that a C/N ratio of 27:1 offers numerous benefits for the cultivation of F. velutipes with comprehensive analyses and has promising application prospects.

Comparison of wear on articular cartilage by titanium alloy, ultra-high-molecular-weight polyethylene, and carbon fibre reinforced polyether-ether-ketone: A pilot study.

Artificial implant materials may articulate against native articular cartilage in certain clinical scenarios and the selection of an implant material that results in the least wear on articular cartilage is preferred to maintain normal joint architecture and function. This project compared the wear on porcine femoral condyles induced by articulation against porcine patellae, titanium alloy (Ti6Al4V), ultra high molecular weight polyethylene (UHMWPE), and carbon fibre reinforced polyether-ether-ketone (CFR-PEEK) through an ex vivo experimental setup. A sinusoidal compressive load of 30-160 N, representing an approximate joint pressure of 0.19-1 MPa at a frequency of 3 Hz coupled with a rotational displacement of +/- 10° at 3 Hz was used to simulate physiological joint motion. Wear was characterized via gross examination and histologically using the OARSI scoring system after 43,200 cycles. CFR-PEEK resulted in the most significant wear on articular cartilage compared to titanium alloy and UHMWPE whereas titanium alloy and UHMWPE resulted in similar levels of wear. All materials caused more wear compared to cartilage-on-cartilage testing. The wear mechanism was characterized by progressive loss of proteoglycan content in cartilage in histology samples.

[Predictive value of diaphragmatic thickening fraction combined with MRC score for the outcome of weaning from mechanical ventilation in ICU-acquired weakness patients].

OBJECTIVE: To explore the predictive value of diaphragmatic thickening fraction (DTF) combined with Medical Research Council-score (MRC score) on the outcome of weaning from mechanical ventilation in ICU-acquired weakness (ICU-AW) patients. METHODS: A retrospective case-control study was conducted. The clinical data of mechanically ventilated patients with an MRC score of less than 48 admitted to the department of critical care medicine of the First Affiliated Hospital of Wannan Medical College from January 2022 to March 2023 were collected, including general information, ultrasound indicators, MRC scores, main clinical outcomes, and weaning outcomes. Patients were divided into successful weaning group and failed weaning group according to whether the patient could maintain effective autonomous breathing for at least 48 hours without using an invasive or non-invasive ventilator. The clinical data of the two groups were compared. Receiver operator characteristic curve (ROC curve) was plotted to analyze the predictive value of DTF and MRC score alone or in combination for successful weaning of patients. RESULTS: A total of 87 patients were enrolled, of which 58 were successful weaning and 29 were failed weaning. There were no statistically significant differences in general data such as gender, age, underlying disease, heart rate (HR), mean arterial pressure (MAP), pH value, blood lactic acid (Lac), oxygenation index (PaO2/FiO2), and severity scores between the two groups. Compared with the failed weaning group, the DTF and MRC scores of patients in the successful weaning group were significantly increased [DTF: (26.02±2.68)% vs. (22.79±5.40)%, MRC score: 38.90±2.78 vs. 33.24±3.78, both P < 0.05]. The duration of mechanical ventilation and the length of ICU stay of patients in the successful weaning group were significantly shorter than those in the failed weaning group [duration of mechanical ventilation (hours): 102.21±32.60 vs. 113.14±41.34, length of ICU stay (days): 6.48±2.18 vs. 10.11±4.01, both P < 0.05], and the re-intubation rate and ICU hospitalization cost were significantly lowered [re-intubation rate: 6.90% (4/58) vs. 27.59% (8/29), ICU hospitalization cost (10 000 RMB): 4.99±0.87 vs. 7.85±2.45, both P < 0.05]. ROC curve analysis showed that the area under the ROC curve (AUC) of DTF and MRC score for predicting successful weaning in ICU-AW mechanical ventilation patients was 0.839 [95% confidence interval (95%CI) was 0.746-0.931] and 0.799 (95%CI was 0.701-0.899), respectively. Using DTF ≥ 25.01% as the optimal cut-off value to predict successful weaning, the sensitivity was 82.76%, and the specificity was 72.41%. Predicting successful weaning based on an optimal cut-off value of MRC score of ≥ 35.50 had a sensitivity of 79.31% and a specificity of 70.69%. Based on the DTF ≥ 25.01% combined with MRC score ≥ 35.50, it was predicted that the weaning would be successful, with an AUC of 0.887 (95%CI was 0.812-0.962), sensitivity increased to 89.70%, and specificity increased to 79.30%. CONCLUSIONS: The DTF and MRC score have good guiding value for the selection of weaning timing and predicting the weaning outcomes in ICU-AW patients. Compared with independent DTF and MRC score, the combination of DTF and MRC score improves the predictive value of successful weaning in ICU-AW patients.

Charge-State-Dependent Collision-Induced Dissociation Behaviors of RNA Oligonucleotides via High-Resolution Mass Spectrometry.

Mass spectrometry (MS)-based analysis of RNA oligonucleotides (oligos) plays an increasingly important role in the development of RNA therapeutics and epitranscriptomics research. However, MS fragmentation behaviors of RNA oligomers are understood insufficiently. Herein, we characterized the negative-ion-mode fragmentation behaviors of 26 synthetic RNA oligos containing four to eight nucleotides using collision-induced dissociation (CID) on a high-resolution, accurate-mass instrument. We found that in CID spectra acquired under the normalized collision energy (NCE) of 35%, approximately 70% of the total peak intensity was attributed to sequencing ions (a-B, a, b, c, d, w, x, y, z), around 25% of the peak intensity came from precursor ions that experienced complete or partial loss of a nucleobase in the form of either a neutral or an anion, and the remainder were internal ions and anionic nucleobases. The top five sequencing ions were the y, c, w, a-B, and a ions. Furthermore, we observed that CID fragmentation behaviors of RNA oligos were significantly impacted by their precursor charge. Specifically, when the precursors had a charge from 1- to 5-, the fractional intensity of sequencing ions decreased, while that of precursors that underwent either neutral or charged losses of a nucleobase increased. Additionally, we found that RNA oligos containing 3'-U tended to produce precursors with HNCO and/or NCO- losses, which presumably corresponded to isocyanic acid and cyanate anion, respectively. These findings provide valuable insights for better comprehending the mechanism behind RNA fragmentation by MS/MS, thereby facilitating the future automated identification of RNA oligos based on their CID spectra in a more efficient manner.

Salidroside Regulates Mitochondrial Homeostasis After Polarization of RAW264.7 Macrophages.

ABSTRACT: Salidroside has anti-inflammatory and antiatherosclerotic effects, and mitochondrial homeostasis imbalance is closely related to cardiovascular disease. The aim of this study was to investigate the effect of salidroside on mitochondrial homeostasis after macrophage polarization and elucidate its possible mechanism against atherosclerosis. RAW264.7 cells were stimulated with 1 µg·mL -1 Lipopolysaccharide and 50 ng·mL -1 IFN-γ establish M1 polarization and were also pretreated with 400 µM salidroside. The relative expression of proinflammatory genes was detected by RT-PCR whereas that of mitochondrial homeostasis-related proteins and nuclear factor kappa-B (NF-κB) was detected by WB. Levels of intracellular reactive oxygen species (ROS), mitochondrial membrane potential, and mass were measured by chemifluorescence whereas that of NF-κB nuclear translocation was detected by immunofluorescence. Compared with the Mφ group, the M1 group demonstrated increased mRNA expression of interleukin-1ß , inductible nitric oxide synthase (iNOS), and tumor necrosis factor-α ; increased protein expression of iNOS, NOD-like receptor protein 3, putative kinase 1 , and NF-κB p65 but decreased protein expression of MFN2, Tom20, and PGC-1α; decreased mitochondrial membrane potential and mass; and increased ROS levels and NF-κB p65 nuclear translocation. Salidroside intervention decreased mRNA expression of interleukin-1ß and tumor necrosis factor-α compared with the M1 group but did not affect that of iNOS. Furthermore, salidroside intervention prevented the changes in protein expression, mitochondrial membrane potential and mass, ROS levels, and NF-κB p65 nuclear translocation observed in the M1 group. In summary, salidroside ultimately inhibits M1 macrophage polarization and maintains mitochondrial homeostasis after macrophage polarization by increasing mitochondrial membrane potential, decreasing ROS levels, inhibiting NF-κB activation, and in turn regulating the expression of proinflammatory factors and mitochondrial homeostasis-associated proteins.

[Emergency treatment of centrifugal pump dysfunction in extracorporeal membrane oxygenation].

OBJECTIVE: To summarize the treatment process of rapid decrease in blood flow due to centrifugal pump dysfunction during extracorporeal membrane oxygenation (ECMO) and its related thinking. METHODS: On September 25, 2021, the ECMO treatment of a 14-year-old boy with severe mycoplasma pneumonia, severe viral pneumonia and acute respiratory distress syndrome (ARDS) admitted to the department of critical care medicine of the First Affiliated Hospital of Wannan Medical College was analyzed. RESULTS: Oxygenation of the child was difficult to maintain under invasive mechanical ventilation, and lung consolidation progressed seriously. After evaluation, venous-venous ECMO (VV-ECMO) was implemented, then oxygenation was improved. In the 120th hour after VV-ECMO establishment, the blood flow sudden decreased, the speed was 3 822 r/min, while the flow was only 0.2 L/min, more over there was no change in the flow when the speed was increased. Before that, the ECMO speed was 3 530 r/min, and the flow was up to 3.4 L/min and stable. After rapid screening, it was determined that the centrifugal pump was dysfunction. ECMO was successfully replaced and the flow was satisfactory. CONCLUSIONS: At present, most ECMO centers do not routinely monitor the pressure before and after the pump. There is a lack of visual and quantitative techniques or indicators to judge the pump's function, and there is also a lack of corresponding clinical experience in treatment. This paper summarizes the investigation and treatment process of ECMO pump dysfunction of this case to provide reference.

Granulin as an important immune molecule involved in lamprey tissue repair and regeneration by promoting cell proliferation and migration.

Progranulin (PGRN) is an autocrine growth factor that regulates cell proliferation, migration, wound healing, and tissue repair in mammals. Lamprey is the most primitive of the extant vertebrates and is regarded as the survivor of a once flourishing group of paleozoic vertebrates, with a history of more than 500 million years. To date, the evolutionary dynamics and the underlying function of the PGRNs remain largely unclear in lamprey. Here, we screened four genes encoding PGRNs from the genomes of Lethenteron reissneri and Petromyzon marinus, including one long form (named Lr-PGRN-L) and three short forms (named Lr-PGRN-S1, Lr-PGRN-S2, and Lr-PGRN-S3), and performed phylogenetic tree, functional domain, and synteny analyses to identify the evolutionary history of the four Lr-PGRNs. In addition, the expressions of the four Lr-pgrn family genes and the immune response against various pathogenic challenges were also investigated. We found that these genes were widely distributed in various tissues of lamprey and performed a variety of functions. Moreover, our results suggest that Lr-PGRN-S1 induces cell migration and proliferation, and is involved in repair after skin and spinal cord injury under appropriate conditions. Our findings are valuable because they improve the understanding of the evolutionary relationship of vertebrate pgrn genes, as well as providing new insights into the diverse and important roles of Lr-PGRNs.

Accurate Proteoform Identification and Quantitation Using pTop 2.0.

The remarkable advancement of top-down proteomics in the past decade is driven by the technological development in separation, mass spectrometry (MS) instrumentation, novel fragmentation, and bioinformatics. However, the accurate identification and quantification of proteoforms, all clearly-defined molecular forms of protein products from a single gene, remain a challenging computational task. This is in part due to the complicated mass spectra from intact proteoforms when compared to those from the digested peptides. Herein, pTop 2.0 is developed to fill in the gap between the large-scale complex top-down MS data and the shortage of high-accuracy bioinformatic tools. Compared with pTop 1.0, the first version, pTop 2.0 concentrates mainly on the identification of the proteoforms with unexpected modifications or a terminal truncation. The quantitation based on isotopic labeling is also a new function, which can be carried out by the convenient and user-friendly "one-key operation," integrated together with the qualitative identifications. The accuracy and running speed of pTop 2.0 is significantly improved on the test data sets. This chapter will introduce the main features, step-by-step running operations, and algorithmic developments of pTop 2.0 in order to push the identification and quantitation of intact proteoforms to a higher-accuracy level in top-down proteomics.

Lamprey immunity protein enables detection for bladder cancer through recognizing N-hydroxyacetylneuraminic acid (Neu5Gc)-modified as a diagnostic marker and exploration of its production mechanism.

Previous studies have demonstrated that Neu5Gc is highly expressed in breast, ovarian, prostate, colon and lung cancers, but not in normal human cells. The presence of Neu5Gc is important for prognosis and is associated with aggressiveness, metastasis, and tumor grade. However, increased Neu5Gc in bladder cancer remains unclear. LIP from lamprey binds the carbohydrate receptor of N-glycolylneuraminic acid (Neu5Gc). The combination of Neu5Gc and LIP suggested that it might be used as a diagnostic tool for the detection of Neu5Gc tumor antigen. Here, the classical animal model of bladder cancer was successfully induced by MNU bladder perfusion. The ELISA results showed that the expression level of Neu5Gc in the urine of normal rats was 94.96 ± 21.01ng/mg, and that of bladder cancer rats was 158.28 ± 34.86 ng/mg. In addition, the results of SNA and LIP immunohistochemistry demonstrated the high expression of Neu5Gc in bladder cancer. After the addition of Neu5Gc to BIU-87 and SV-HUC-1 cells, transcriptomic sequencing and real-time quantitative PCR analysis demonstrated that the gene expression of Neu5Gc synthesis pathway was significantly increased. These data suggest that LIP provides a new tool for the detection of biological samples, especially urine from patients with bladder cancer or suspected cancer, and that revealing the mechanism of abnormal glycosylation can provide theoretical basis for clinical studies.

Prevalence and risk factors for intensive care unit acquired weakness: A protocol for a systematic review and meta-analysis.

BACKGROUND: Intensive care unit-acquired weakness (ICU-AW) is an acquired neuromuscular lesion and a common occurrence in patients who are critically ill. We will systematically summarize and incorporate the important risk factors and prevalence from previously published multivariate analyses for ICU-AW. METHODS: We will search the PubMed, Embase, Web of Science, and the Cochrane library to identify the relevant studies about the prevalence and risk factors for ICU-AW. Two reviewers will independently review the studies for eligibility according to the inclusion criteria. Two reviewers will independently assess the quality of studies by using the Newcastle-Ottawa scale for nonrandomized studies. Heterogeneity among studies will be estimated by the I statistic. RESULTS: This systematic review and meta-analysis will provide an evidence of prevalence and risk factors for the ICU-AW. CONCLUSION: We hope that our research will contribute to clinicians and public decision making about the ICU-AW.

Intensive care unit acquired weakness: A protocol for an overview of systematic reviews and meta-analysis.

BACKGROUND: Intensive care unit-acquired weakness (ICU-AW) is an acquired neuromuscular lesion and a common occurrence in patients who are critically ill. There are already systematic reviews on ICU-AW. Therefore, we provide a protocol for an overview of systematic reviews to improve the effectiveness of the construction of an evidence-based practice for prevention of ICU-AW. METHODS: We will search the PubMed, CINAHL, EMBASE, and the Cochrane Library for the relevant systematic review or meta-analyses about ICU-AW. Study selection, data extraction, and the quality assessment of the included studies will be performed independently by 2 reviewers. And the methodological quality, report quality and evidence quality will be evaluated by Assessment of Multiple Systematic Reviews-2 tool, Preferred Reporting Items for Systematic Reviews and Meta Analyses Statement checklist and Grading of Recommendations Assessment, Development and Evaluation system, respectively. RESULTS: This overview of systematic reviews and meta-analysis will collect the evidence published about the ICU-AW. CONCLUSION: We hope that our research will contribute to clinicians and public decision making about the ICU-AW. REGISTRATION NUMBER: INPLASY202070067.

MASH Explorer: A Universal Software Environment for Top-Down Proteomics.

Top-down mass spectrometry (MS)-based proteomics enable a comprehensive analysis of proteoforms with molecular specificity to achieve a proteome-wide understanding of protein functions. However, the lack of a universal software for top-down proteomics is becoming increasingly recognized as a major barrier, especially for newcomers. Here, we have developed MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database search algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time. It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide. With the critical need and tremendous support from the community, we envision that this MASH Explorer software package will play an integral role in advancing top-down proteomics to realize its full potential for biomedical research.

Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers.

Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially.

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides.

We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, 15N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.

Global Quantification of Intact Proteins via Chemical Isotope Labeling and Mass Spectrometry.

Although thousands of intact proteins have been feasibly identified in recent years, global quantification of intact proteins is still challenging. Herein, we develop a high-throughput strategy for global intact protein quantification based on chemical isotope labeling. The isotope incorporation efficiency is as high as 99.2% for complex intact protein samples extracted from HeLa cells. Further, the pTop 2.0 software is developed for automated quantification of intact proteoforms in a high-throughput manner. The high quantification accuracy and reproducibility of this strategy have been demonstrated for both standard and complex cellular protein samples. A total of 2283 intact proteoforms originated from 660 protein accessions are successfully quantified under anaerobic and aerobic conditions and the differentially expressed proteins are observed to be involved in the important biological processes such as stress response.

Small Cell Carcinoma of the Hypopharynx.

Small cell carcinoma is rarely found to originate from the hypopharynx and there exists no treatment guidelines due to the small number of cases. Here, we present a case of a female patient with metastatic small cell carcinoma originating from the posterior hypopharynx with lymph node involvement. Her treatment consisted of chemotherapy with etoposide and cisplatin as well as radiation therapy. Her post-treatment computed tomography (CT) scan indicated resolution of the disease at the primary site and follow-up positron emission tomography (PET)-CT scan at three-month post radiation therapy revealed that the patient is clear of the disease.